All Questions

41
votes
0answers
754 views

How can I update a map/mesh and coordinates in a PyMol session file?

I have a PyMol session file I was using to create my figures. It contains a protein and ligand broken into several groups of atoms with a fair bit of overlap. There are also a few meshes built from ...
20
votes
0answers
168 views

Synthesis Golf X: TAK-457

I shall try to revive this! A full FAQ post has been written on chemistry.meta.SE, explaining the premise of synthesis golf and the 'rules'. Please take a look at this before answering (if you haven't ...
17
votes
0answers
194 views

Single-molecule magnet with electrically-controlled permeability: How does the Titan Shield from Deus Ex work?

In a recent installment of Deus Ex game series there is an augmentation called "Titan Shield" (it has nothing to do with $\ce{Ti}$ element): A neodymium skin underlay matrix built of nano-meshed ...
16
votes
0answers
377 views

Ambimodal transition states in some organic reaction pathways

In many computational studies, mechanisms appear to have so-called ambimodal transition states, i.e. a transition state which can lead to multiple products, in conflict to the common undergraduate ...
15
votes
0answers
331 views

How does the cyclopropyl group influence conjugation and aromaticity?

While answering the question Why isn't cyclobutane planar?, I recollected that cyclopropane and its derivatives behave like double-bond compounds, e.g. a cyclopropyl group can potentially be ...
15
votes
0answers
214 views

f-electrons in chemistry of heavy transition metals

In one lecture on recent MCR-X conference I was puzzled by a side-note "f-hole is critical to describe DoS of $\ce{IrO2}$ correctly." The context was DFT periodic plane-wave calculations with ...
14
votes
0answers
112 views

Is there a consensus on whether amber can seal in air bubbles for millions of years?

I read about deriving the oxygen content in the atmosphere in the Cretaceous by analyzing the air trapped in bubbles in amber from that period, but I have also found papers disputing the study's ...
14
votes
0answers
1k views

How to Calculate Transition Dipole Moment from Two Known Wavefunctions

I am interested in calculating the transition dipole moment (TDM) from the information from two wavefunctions of different states. This is somewhat similar to calculating the molecular dipole moment ...
13
votes
0answers
7k views

Melting and boiling point trend in Group II

The following picture shows the melting and boiling point trends down group II elements. I have added question marks where the variability in data was rather disturbing (over two hundred degrees ...
13
votes
0answers
689 views

Neighbouring group participation with and without retention of configuration in nucleophilic substitution of 2,6-dichloro-9-thiabicyclo[3.3.1]nonane

Treatment of the dichloride A under the conditions indicated gives B with retention of configuration, while treatment of dichloride C gives D with inversion of configuration. I am having ...
12
votes
0answers
185 views

Why does a Diels–Alder reaction not occur here?

I have recently come across this organic chemistry problem. I thought it would undergo simple Diels–Alder reaction But it didn't turn out to be. The product to me looks like a nucleophilic attack ...
12
votes
0answers
169 views

Verifying data acquired from a molecular dynamics simulation

This question is about verifying a system simulated with MD. I am currently building a model of a two phase gas-liquid system, where I initially have $\ce{N2}$, $\ce{CO2}$, $\ce{Ar}$, $\ce{He}$ and $\...
12
votes
0answers
274 views

What was the lithium concentration in 1940's 7-Up?

I just came across this article in the New York Times, where lithium (or more correctly, lithium salts), a known anti-depressant had been added to beverages in the 1940's. They also mention that a ...
11
votes
0answers
96 views

Tetrahedrane Properties and Analogs

I took a look into some tetrahedrane (C4H4) analogs, platonic hydrocarbon, basically very strained tetrahedral geometry at every carbon. I was wondering what will be the predicted delta H of ...
11
votes
0answers
172 views

Why is Diiron nonacarbonyl so exceptional?

My textbooks says: With exception of $\ce{Fe2(CO)9}$, all other metal carbonyls are soluble in hydrocarbon solvents. Weller, M.; Overton, T.; Rourke, J.; Armstrong, F. Inorganic Chemistry, 6th ed. ...
11
votes
0answers
133 views

Estimating stability and mean life of anomalous tautomers

A pair of bases in the DNA, say, A-T, have a tautomerized form A*-T* (resulting from switching the sides of both protons along the hydrogen bridges). I have studied how, by means of DFT computations, ...
11
votes
0answers
227 views

Rotation around CC bond in 1,2-dioxetane: transition states and local minimum structures

TLDR: What: Potential energy surface associated with rotation around CC bond in the ring-opened version of 1,2-dioxetane. How: State average(4)-CASSCF(12,10)/VTZP constrained geometry optimizations ...
11
votes
0answers
192 views

Density Functional Theory with Generalized Gradient Approxmations (GGA) - What Happens if the Electron Density Shows a “Kink” at the Ion Position?

My question may be stupid, so please correct me if you find anything which is obviously erroneous. In the following I will place a question mark (?) besides points/steps I consider doubtful. My ...
10
votes
0answers
122 views

Products formed on cleavage of epoxides using HI

There seems to be multiple forms of HI used to cleave epoxides: conc. HI, anhydrous HI, cold HI, hot HI, cold conc. HI, hot conc. HI, etc. So, does concentration of HI and temperature have any ...
10
votes
0answers
85 views

In a molecular dynamics context, is the methyl rotation in propene a symmetric or asymmetric internal rotor?

In a prior question, I asked about the (a)symmetry of the potential energy surface of the methyl rotation of propene. In that context, the kinetic energy of the nuclear motions is of course assumed ...
10
votes
0answers
153 views

Obtaining activity coefficients of conjugate acids of some common carboxylic acid molecules

Recently, I have been wondering about justifying the notion on how some common acids (e.g. carboxylic acids) are themselves weaker bases than water to the point that we don't usually consider them to ...
10
votes
0answers
98 views

Mechanistic Explanation of Circular Dichroism

I'm wondering if someone can give me a physically motivated reason for why chiral molecules interact with left and right circularly polarized light (LCP) (RCP) differently. Particularly, a quantum ...
10
votes
0answers
61 views

Is there a structured data source containing information on the World Health Organisation's Stability Testing Policies?

Hoping to automate some product testing guidance software, I've been attempting to find a (hopefully live, up-to-date) Database, Web-service, or other structured data source containing the ...
10
votes
0answers
114 views

Color of methoxy substituted phenyl rings when heated in the presence of acid

Anyone who's familiar with organic synthesis will probably have came across the DMB and PMB protecting groups. When TLC-ing compounds containing these protecting groups using common stains like ...
10
votes
0answers
18k views

Reaction of phenol with Zinc dust

I have seen this reaction many times: $\text {Phenol}+\text{Zn}\ce {->}\text{Benzene}+\text{ZnO} $ But what is the mechanism?! Tried a lot but couldn't cook up one... Thanks for any help...
9
votes
0answers
58 views

Explanation of the strength of phosphorus-oxygen bond

When discussing the Wittig reaction, Clayden's Organic Chemistry cites the strength of the $\ce{P=O}$ formed in triphenylphosphine oxide as a driver of the reaction through enthalpy: The $\ce{P=O}$ ...
9
votes
0answers
104 views

Does this binary compound of C and N - isoelectronic with carbon suboxide - exist?

I am a mathematician not a chemist, so my questions are naive and rather combinatorial. I am intrigued by the possibility of the following compound: $$\ce{N- = N+ = C = N+ = N-}$$ which ought to ...
9
votes
0answers
138 views

Protonating/basic site and Brønsted basicity orders of beta, gamma, and delta lactams

Consider the three cyclic amides: $\beta$-lactam $\gamma$-lactam $\delta$-lactam My question What is the basic site (site of protonation) for these three lactams? And what should be their Brønsted ...
9
votes
0answers
75 views

How sure can we be about the structure of purine?

While answering the question Basicities of nitrogen atoms in purine, I noticed, that there might be a rapid interchange of the hydrogen bonded to the nitrogen atoms. I have found a crystal structure ...
9
votes
0answers
109 views

What kind of chemical used in a chromatography run could be denoted with the letters D.H.?

A fellow translator is having trouble translating (into Russian) the mysterious D.H. abbreviation in the following passage: Slight variations of the ratio of the mobile phase constituents or ...
9
votes
0answers
195 views

What are these “certain chemical compounds” denser than osmium?

The Wikipedia entry for density states Osmium and iridium are the densest known elements at standard conditions for temperature and pressure but certain chemical compounds may be denser. I ...
9
votes
0answers
133 views

Aza-enolates: why no reaction at N

My understanding is that aza-enolates have an advantage over enamines in enolate-type alkylations because the reaction at N is less likely. As a result, unactivated electrophiles can be used (i.e. ...
9
votes
0answers
202 views

2017 Nobel Prize; What does Cryo-electron microscopy data actually look like?

It was just announced that the 2017 Nobel Prize for Chemistry has been awarded to Jacques Dubochet, Joachim Frank and Richard Henderson "for developing cryo-electron microscopy for the high-...
9
votes
0answers
65 views

Would cerium(III) in solution be oxidized to cerium(IV) in ESI mass spectroscopy?

During ESI (assuming positve ion mode for now), we apply a strong voltage ($1.0{-}\pu{5.0 kV}$) to induce ionization. Therefore, it is common to see oxidation of metal ions (e.g. $\ce{Cu^{+I} -> ...
9
votes
0answers
73 views

Physical meaning of thermal parameters dimension (Ų)

In single-crystal x-ray crystallography both isotropic and anisotropic displacement parameters $U_{ij}$ of thermal ellipsoids have dimension of square angstrom ($Å^2$) as follows from the definition ...
9
votes
0answers
132 views

Accuracy of quantum chemistry calculations on iodine neglecting relativistic effects

Triiodothyronine is a molecule with three iodine atoms. If we attempted to calculate its properties with ab initio methods like Hartree-Fock or more complicated ab initio methods which included ...
9
votes
0answers
92 views

Some materials emit more photoelectrons than others - why?

Again, I'm a physicist turning to chemists (so bear with me). So I've been measuring some materials by changing the wavelength of the incident light on the material and I have a detecting tip like in ...
9
votes
0answers
1k views

Synthesis of Anthracene: Mechanism

Recently, I happened to find a problem that involved the synthesis of anthracene from bromobenzene in the presence of tert-butyl lithium, using THF as the solvent, and at room temperature. I am ...
9
votes
0answers
92 views

Newer ionic radii data than Shannon's 1976 compilation?

Shannon, R. D., 1976, Revised effective ionic radii and systematic studies of interatomic distances in halides and chalcogenides: Acta Crystallographica Section A, v. 32, p. 751–767. DOI: 10.1107/...
9
votes
0answers
162 views

Transition state optimisation on the surface of periclase

I want to model a reaction catalysed by periclase ($\ce{MgO}$) using DFT. I have a good guess on the transition state (TS) of the reaction that goes in gas phase/solvent (produced using MOPAC). The ...
9
votes
0answers
91 views

How to color bonds by the strain?

I need to create a figure of a molecule in which the bonds are colored in a RGB scale according to the values read from a data file. The data file contains, for example, the increase or decrease in ...
9
votes
0answers
552 views

What exactly is the Horwitz equation?

During a laboratory exercise in a course on analytical chemistry, we were asked to calculate the $z$-score. $$z=\frac{X_{\text{lab}}-X_{\text{cons}}}{S_{\text{target}}}$$ where $X_{\text{...
9
votes
0answers
81 views

Which potentials are suitable for molecular dynamics simulation of simple explicit solvents?

Which potentials (force fields) are suitable for adequately simulating (mixtures of) explicit solvents? Interesting rheological properties include viscosity, surface tension, heat capacity.
9
votes
0answers
151 views

Does a cationic 1,3-triphosphinane react with a methyl cation?

The question is: Reaction of $\ce{Et2P(CH2)3PEt2}\text{ with }\ce{PCl3}$ ($1:1$) in the presence of $\ce{SnCl2}$ gives a ring system A, which exhibits two phosporus NMR resonances, a doublet and a ...
9
votes
0answers
414 views

Orbital and state correlation diagram for ring-closure of pentadienyl to a cyclic allyl

This is an exam question. I am to construct the orbital and state correlation diagram for one of the reaction below (disrotation or conratation). Also, I should explain whether the reaction is ...
9
votes
0answers
780 views

Nucleophilicity/basicity in protic and aprotic solvents

In polar aprotic solvent, why is $\ce{F-}$ a stronger nucleophile than $\ce{I-}$? What I think: If I talk about their basicity, $\ce{F-}$ would be more basic due to instability from its high electron ...
9
votes
0answers
164 views

What is the difference between Fukui FMO approach and Woodward-Hoffmann rules?

If I understand correctly Frontier MO-theory is based on the perturbation theory of reactivity and the Woodward-Hoffmann rules consider conservation of orbital symmetry. Does FMO use symmetry ...
9
votes
0answers
537 views

Mixing two containers of each water and ethanol to varying degrees of purity

In the following question, the water/wine mixing problem was recast in chemical terms. However, partial molar volumes can make this a much more challenging problem than it appears on the surface. ...
9
votes
0answers
367 views

Free Web-Based Orbital Solver to look into the Walsh orbitals of a perturbed cyclopropane

There exists a free online orbital calculator. When I draw cyclopropane it plots three molecular orbitals, but unfortunately it doesn't use the Walsh orbitals. Are there any free online tools which ...
9
votes
0answers
643 views

Can I make Ferrofluid without evaporating Ammonium?

I want to make ferrofluid, which is ferromagnetic particles suspended in a carrier fluid. Three methods I have seen involve using magnetic ink (for MICR codes), cassette tapes, or ferric chloride as ...

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